Population structure limits inferences from genomic prediction and genome-wide association studies in a forest tree DOI Creative Commons
Gancho T. Slavov, David Macaya‐Sanz, Stephen DiFazio

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 12, 2024

Abstract There is overwhelming evidence that forest trees are locally adapted to climate. Thus, genecological models based on population phenotypes have been used measure local adaptation, assess risks of genetic maladaptation climate, and guide assisted migration. However, instead phenotypes, there increasing interest in using genomic data for gene resource management. We whole-genome resequencing a replicated common- garden experiment understand the architecture adaptive traits black cottonwood. studied potential genome-wide association studies (GWAS) prediction detect causal loci, identify climate-adapted practice analyzed hierarchical structure by partitioning phenotypic (SNP) variation among 840 genotypes collected from 91 stands along 16 rivers. Most (60-81%) occurred at level was strongly associated with Population were predicted well (e.g., predictive ability r > 0.9) but almost as climate or geography ( 0.8). In contrast, within populations poor < 0.2). Similarly, we identified many GWAS associations populations, most appeared be spurious pooled within-population analyses. Hierarchical linkage disequilibrium haplotype sharing suggested because allele frequencies loci linked markers differed populations. Our results highlight difficulty when structure, limitations information alone

Language: Английский

The Evolutionary Reasons of Epigenetics DOI Creative Commons
Giorgio Camilloni

DNA, Journal Year: 2025, Volume and Issue: 5(1), P. 6 - 6

Published: Jan. 30, 2025

Epigenetic modifications affecting DNA, RNA, and proteins can alter the functional state of a gene heavily interfere with expression. These processes are typically transient, predominant form inheritance is mitotic, small fraction transgenerational modifications. It therefore reasonable to ask what forces drive this acquisition in living beings, where certain variations phenotype do not correspond changes DNA sequence.

Language: Английский

Citations

0
The chromosome-scale genomes of two Tinospora species reveal differential regulation of the MEP pathway in terpenoid biosynthesis DOI Creative Commons
Zhiyu Chen, Xun Lan,

Yunyan Lu

et al.

BMC Biology, Journal Year: 2025, Volume and Issue: 23(1)

Published: March 20, 2025

The relationship between gene family expansion and the resulting changes in plant phenotypes has shown remarkable complexity during evolution. contributed to diversity phenotypes, specifically metabolites through neo-functionalization sub-functionalization. However, negative regulatory effects associated with remain poorly understood. Here, we present chromosome-scale genomes of Tinospora crispa sinensis. Comparative genomic analyses demonstrated conserved chromosomal evolution within Menispermaceae family. KEGG analysis revealed a significant enrichment genes related terpenoid biosynthesis T. exhibited higher abundance terpenoids compared Detailed encoding 1-hydroxy-2-methyl 2-(E)-butenyl 4-diphosphate synthase (HDS), key enzyme 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway TsiHDS4 retained ancestral function converting methylerythritol cyclic diphosphate (MEcPP) (E)-4-hydroxy-3-methylbut-2-enyl (HMBPP). noncanonical CDS-derived small peptide TsiHDS5 was interact TsiHDS4, inhibiting its catalytic activity. This interaction reduced levels HMBPP isopentenyl pyrophosphate (IPP), which represent substrates for downstream biosynthesis. These findings offer clues decipher variations MEP sinensis form basis further detailed research on regulation expanded genes.

Language: Английский

Citations

0
Distantly related bacteria share a rigid proteome allocation strategy with flexible enzyme kinetics DOI Creative Commons
Manlu Zhu, Matteo Mori, Terence Hwa

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(18)

Published: April 29, 2025

Bacteria are known to allocate their proteomes according how fast they grow, and the allocation strategies employed strongly affect bacterial adaptation different environments. Much of what is currently about proteome based on extensive studies model organism Escherichia coli . It not clear much E. ’s strategy applicable other species, particularly since species can grow at vastly rates even in same growth condition. In this study, we investigate differences nutrient-dependent programs adopted by several distantly related including Vibrio natriegens , one fastest-growing bacteria known. Extensive quantitative characterization across conditions reveals an invariant program response changing nutrients despite systemic, species-specific enzyme kinetics. This organized rate but a common internal metric nutrient quality after scaling away kinetics, with faster behaving as if it growing under higher temperature. The flexibility kinetics rigidity defy notions evolvability resource optimization. Our results suggest existence blueprint shared diverse implications underlying regulatory strategies. Further knowledge organization such phylogeny-transcending relations also promises simplify bottom–up description understanding behaviors ecological communities.

Language: Английский

Citations

0
Long Noncoding RNAs in Response to Hyperosmolarity Stress, but Not Salt Stress, Were Mainly Enriched in the Rice Roots DOI Open Access

Pang Yanrong,

Kaifeng Zheng, Qinyue Min

et al.

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(11), P. 6226 - 6226

Published: June 5, 2024

Due to their immobility and possession of underground parts, plants have evolved various mechanisms endure adapt abiotic stresses such as extreme temperatures, drought, salinity. However, the contribution long noncoding RNAs (lncRNAs) different distinct rice seedling parts remains largely uncharacterized beyond protein-coding gene (PCG) layer. Using transcriptomics bioinformatics methods, we systematically identified lncRNAs characterized expression patterns in roots shoots wild type (WT) ososca1.1 (reduced hyperosmolality-induced [Ca2+]i increase rice) seedlings under hyperosmolarity salt stresses. Here, 2937 candidate were seedlings, with intergenic representing largest category. Although detectable sequence conservation was low, observed that had more orthologs within Oryza. By comparing WT ososca1.1, transcription level OsOSCA1.1-related greatly enhanced face hyperosmolality stress. Regarding regulation mode, co-expression network revealed connections between trans-regulated target PCGs related OsOSCA1.1 its mediation stress sensing. Interestingly, compared PCGs, sensitive than Furthermore, stress-responsive enriched roots, potential cis-regulated genes associated transcriptional signaling transduction. Not be ignored, a motif-conserved stress-activated lncRNA (OSlncRNA), speculating on origin evolutionary history In summary, provide global perspective resource understand sensing which helps decode complex molecular networks involved plant adaptation stressful environments.

Language: Английский

Citations

1
Population structure limits inferences from genomic prediction and genome-wide association studies in a forest tree DOI Creative Commons
Gancho T. Slavov, David Macaya‐Sanz, Stephen DiFazio

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 12, 2024

Abstract There is overwhelming evidence that forest trees are locally adapted to climate. Thus, genecological models based on population phenotypes have been used measure local adaptation, assess risks of genetic maladaptation climate, and guide assisted migration. However, instead phenotypes, there increasing interest in using genomic data for gene resource management. We whole-genome resequencing a replicated common- garden experiment understand the architecture adaptive traits black cottonwood. studied potential genome-wide association studies (GWAS) prediction detect causal loci, identify climate-adapted practice analyzed hierarchical structure by partitioning phenotypic (SNP) variation among 840 genotypes collected from 91 stands along 16 rivers. Most (60-81%) occurred at level was strongly associated with Population were predicted well (e.g., predictive ability r > 0.9) but almost as climate or geography ( 0.8). In contrast, within populations poor < 0.2). Similarly, we identified many GWAS associations populations, most appeared be spurious pooled within-population analyses. Hierarchical linkage disequilibrium haplotype sharing suggested because allele frequencies loci linked markers differed populations. Our results highlight difficulty when structure, limitations information alone

Language: Английский

Citations

0